Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics
Motivation Gene expression is characterized by stochastic bursts of transcription that occur
at brief and random periods of promoter activity. The kinetics of gene expression burstiness …
at brief and random periods of promoter activity. The kinetics of gene expression burstiness …
Trajectorynet: A dynamic optimal transport network for modeling cellular dynamics
It is increasingly common to encounter data in the form of cross-sectional population
measurements over time, particularly in biomedical settings. Recent attempts to model …
measurements over time, particularly in biomedical settings. Recent attempts to model …
Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data
Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology to determine the
precise gene expression of individual cells and identify cell heterogeneity and …
precise gene expression of individual cells and identify cell heterogeneity and …
Alignment of single-cell trajectories to compare cellular expression dynamics
A Alpert, LS Moore, T Dubovik, SS Shen-Orr - Nature methods, 2018 - nature.com
Single-cell RNA sequencing and high-dimensional cytometry can be used to generate
detailed trajectories of dynamic biological processes such as differentiation or development …
detailed trajectories of dynamic biological processes such as differentiation or development …
LineageOT is a unified framework for lineage tracing and trajectory inference
A Forrow, G Schiebinger - Nature communications, 2021 - nature.com
Understanding the genetic and epigenetic programs that control differentiation during
development is a fundamental challenge, with broad impacts across biology and medicine …
development is a fundamental challenge, with broad impacts across biology and medicine …
Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
J Ding, A Regev - Nature communications, 2021 - nature.com
Abstract Single-cell RNA-Seq (scRNA-seq) is invaluable for studying biological systems.
Dimensionality reduction is a crucial step in interpreting the relation between cells in scRNA …
Dimensionality reduction is a crucial step in interpreting the relation between cells in scRNA …
Modelling and simulating generic RNA-Seq experiments with the flux simulator
High-throughput sequencing of cDNA libraries constructed from cellular RNA complements
(RNA-Seq) naturally provides a digital quantitative measurement for every expressed RNA …
(RNA-Seq) naturally provides a digital quantitative measurement for every expressed RNA …
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
PC Aubin-Frankowski, JP Vert - Bioinformatics, 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) offers new possibilities to infer gene
regulatory network (GRNs) for biological processes involving a notion of time, such as cell …
regulatory network (GRNs) for biological processes involving a notion of time, such as cell …
Mapping translation'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes
Messenger RNA localization is important for cell motility by local protein translation.
However, while single mRNAs can be imaged and their movements tracked in single cells, it …
However, while single mRNAs can be imaged and their movements tracked in single cells, it …